Literature DB >> 15527337

Model for small-sample bias of free-energy calculations applied to Gaussian-distributed nonequilibrium work measurements.

Di Wu1, David A Kofke.   

Abstract

We present a model for the bias of free-energy differences when determined using the nonequilibrium work (NEW) formalism due to Jarzynski. Input to the model is the distribution of work values underlying the NEW calculation, and the bias is estimated by assuming that all of the inaccuracy is incurred by failure to sample work values beyond a specific point in the tail of the distribution. The model is formulated considering both small- and large-sample NEW calculations. It is then applied to the study of bias for cases in which the work distribution is Gaussian. The model is shown to give an excellent description of the bias in situations where the bias is a more significant source of error than the sample variance. A scaling law is presented and it is shown that the bias as a function of sampling can be reduced to a single universal curve, approximately valid for all Gaussian work distributions. This result is used to formulate a simple criterion that can be applied to test if a NEW calculation is effectively free of bias. The criterion is shown to be effective even though it uses the measured (and perhaps biased) free energy as an input. Copyright 2004 American Institute of Physics.

Mesh:

Year:  2004        PMID: 15527337     DOI: 10.1063/1.1806413

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  6 in total

1.  Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Authors:  Paul Maragakis; Felix Ritort; Carlos Bustamante; Martin Karplus; Gavin E Crooks
Journal:  J Chem Phys       Date:  2008-07-14       Impact factor: 3.488

2.  Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches.

Authors:  Phillip S Hudson; Félix Aviat; Rubén Meana-Pañeda; Luke Warrensford; Benjamin C Pollard; Samarjeet Prasad; Michael R Jones; H Lee Woodcock; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2022-05-22       Impact factor: 4.179

3.  Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2019-09-17       Impact factor: 6.006

4.  Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching.

Authors:  Xiaoliang Pan; Pengfei Li; Junming Ho; Jingzhi Pu; Ye Mei; Yihan Shao
Journal:  Phys Chem Chem Phys       Date:  2019-09-11       Impact factor: 3.676

5.  Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale.

Authors:  Phillip S Hudson; Kyungreem Han; H Lee Woodcock; Bernard R Brooks
Journal:  J Comput Aided Mol Des       Date:  2018-10-01       Impact factor: 3.686

6.  The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations.

Authors:  Fiona L Kearns; Luke Warrensford; Stefan Boresch; H Lee Woodcock
Journal:  Molecules       Date:  2019-02-14       Impact factor: 4.411

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.